.TH pdb2gmx 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5"
.SH NAME
pdb2gmx - converts pdb files to topology and coordinate files

.B VERSION 4.5
.SH SYNOPSIS
\f3pdb2gmx\fP
.BI "\-f" " eiwit.pdb "
.BI "\-o" " conf.gro "
.BI "\-p" " topol.top "
.BI "\-i" " posre.itp "
.BI "\-n" " clean.ndx "
.BI "\-q" " clean.pdb "
.BI "\-[no]h" ""
.BI "\-[no]version" ""
.BI "\-nice" " int "
.BI "\-chainsep" " enum "
.BI "\-ff" " string "
.BI "\-water" " enum "
.BI "\-[no]inter" ""
.BI "\-[no]ss" ""
.BI "\-[no]ter" ""
.BI "\-[no]lys" ""
.BI "\-[no]arg" ""
.BI "\-[no]asp" ""
.BI "\-[no]glu" ""
.BI "\-[no]gln" ""
.BI "\-[no]his" ""
.BI "\-angle" " real "
.BI "\-dist" " real "
.BI "\-[no]una" ""
.BI "\-[no]ignh" ""
.BI "\-[no]missing" ""
.BI "\-[no]v" ""
.BI "\-posrefc" " real "
.BI "\-vsite" " enum "
.BI "\-[no]heavyh" ""
.BI "\-[no]deuterate" ""
.BI "\-[no]chargegrp" ""
.BI "\-[no]cmap" ""
.BI "\-[no]renum" ""
.BI "\-[no]rtpres" ""
.SH DESCRIPTION
\&This program reads a pdb (or gro) file, reads
\&some database files, adds hydrogens to the molecules and generates
\&coordinates in Gromacs (Gromos), or optionally pdb, format
\&and a topology in Gromacs format.
\&These files can subsequently be processed to generate a run input file.
\&


\&pdb2gmx will search for force fields by looking for
\&a \fB forcefield.itp\fR file in subdirectories \fB forcefield.ff\fR
\&of the current working directory and of the Gomracs library directory
\&as inferred from the path of the binary or the \fB GMXLIB\fR environment
\&variable.
\&By default the forcefield selection is interactive,
\&but you can use the \fB \-ff\fR option to specify one of the short names
\&in the list on the command line instead. In that case pdb2gmx just looks
\&for the corresponding \fB forcefield.ff\fR directory.
\&


\&After choosing a force field, all files will be read only from
\&the corresponding force field directory.
\&If you want to modify or add a residue types, you can copy the force
\&field directory from the Gromacs library directory to your current
\&working directory. If you want to add new protein residue types,
\&you will need to modify residuetypes.dat in the libary directory
\&or copy the whole library directory to a local directory and set
\&the environment variable \fB GMXLIB\fR to the name of that directory.
\&Check chapter 5 of the manual for more information about file formats.
\&


\&Note that a pdb file is nothing more than a file format, and it
\&need not necessarily contain a protein structure. Every kind of
\&molecule for which there is support in the database can be converted.
\&If there is no support in the database, you can add it yourself.


\&The program has limited intelligence, it reads a number of database
\&files, that allow it to make special bonds (Cys\-Cys, Heme\-His, etc.),
\&if necessary this can be done manually. The program can prompt the
\&user to select which kind of LYS, ASP, GLU, CYS or HIS residue she
\&wants. For LYS the choice is between neutral (two protons on NZ) or
\&protonated (three protons, default), for ASP and GLU unprotonated
\&(default) or protonated, for HIS the proton can be either on ND1,
\&on NE2 or on both. By default these selections are done automatically.
\&For His, this is based on an optimal hydrogen bonding
\&conformation. Hydrogen bonds are defined based on a simple geometric
\&criterium, specified by the maximum hydrogen\-donor\-acceptor angle
\&and donor\-acceptor distance, which are set by \fB \-angle\fR and
\&\fB \-dist\fR respectively.


\&The separation of chains is not entirely trivial since the markup
\&in user\-generated PDB files frequently varies and sometimes it
\&is desirable to merge entries across a TER record, for instance
\&if you want a disulfide bridge or distance restraints between
\&two protein chains or if you have a HEME group bound to a protein.
\&In such cases multiple chains should be contained in a single
\&\fB molecule_type\fR definition.
\&To handle this, pdb2gmx has an option \fB \-chainsep\fR so you can
\&choose whether a new chain should start when we find a TER record,
\&when the chain id changes, combinations of either or both of these
\&or fully interactively.


\&pdb2gmx will also check the occupancy field of the pdb file.
\&If any of the occupancies are not one, indicating that the atom is
\&not resolved well in the structure, a warning message is issued.
\&When a pdb file does not originate from an X\-Ray structure determination
\&all occupancy fields may be zero. Either way, it is up to the user
\&to verify the correctness of the input data (read the article!).


\&During processing the atoms will be reordered according to Gromacs
\&conventions. With \fB \-n\fR an index file can be generated that
\&contains one group reordered in the same way. This allows you to
\&convert a Gromos trajectory and coordinate file to Gromos. There is
\&one limitation: reordering is done after the hydrogens are stripped
\&from the input and before new hydrogens are added. This means that
\&you should not use \fB \-ignh\fR.


\&The \fB .gro\fR and \fB .g96\fR file formats do not support chain
\&identifiers. Therefore it is useful to enter a pdb file name at
\&the \fB \-o\fR option when you want to convert a multichain pdb file.
\&


\&The option \fB \-vsite\fR removes hydrogen and fast improper dihedral
\&motions. Angular and out\-of\-plane motions can be removed by changing
\&hydrogens into virtual sites and fixing angles, which fixes their
\&position relative to neighboring atoms. Additionally, all atoms in the
\&aromatic rings of the standard amino acids (i.e. PHE, TRP, TYR and HIS)
\&can be converted into virtual sites, elminating the fast improper dihedral
\&fluctuations in these rings. Note that in this case all other hydrogen
\&atoms are also converted to virtual sites. The mass of all atoms that are
\&converted into virtual sites, is added to the heavy atoms.


\&Also slowing down of dihedral motion can be done with \fB \-heavyh\fR
\&done by increasing the hydrogen\-mass by a factor of 4. This is also
\&done for water hydrogens to slow down the rotational motion of water.
\&The increase in mass of the hydrogens is subtracted from the bonded
\&(heavy) atom so that the total mass of the system remains the same.
.SH FILES
.BI "\-f" " eiwit.pdb" 
.B Input
 Structure file: gro g96 pdb tpr etc. 

.BI "\-o" " conf.gro" 
.B Output
 Structure file: gro g96 pdb etc. 

.BI "\-p" " topol.top" 
.B Output
 Topology file 

.BI "\-i" " posre.itp" 
.B Output
 Include file for topology 

.BI "\-n" " clean.ndx" 
.B Output, Opt.
 Index file 

.BI "\-q" " clean.pdb" 
.B Output, Opt.
 Structure file: gro g96 pdb etc. 

.SH OTHER OPTIONS
.BI "\-[no]h"  "no    "
 Print help info and quit

.BI "\-[no]version"  "no    "
 Print version info and quit

.BI "\-nice"  " int" " 0" 
 Set the nicelevel

.BI "\-chainsep"  " enum" " id_or_ter" 
 Condition in PDB files when a new chain and molecule_type should be started: \fB id_or_ter\fR, \fB id_and_ter\fR, \fB ter\fR, \fB id\fR or \fB interactive\fR

.BI "\-ff"  " string" " select" 
 Force field, interactive by default. Use \-h for information.

.BI "\-water"  " enum" " select" 
 Water model to use: \fB select\fR, \fB none\fR, \fB spc\fR, \fB spce\fR, \fB tip3p\fR, \fB tip4p\fR or \fB tip5p\fR

.BI "\-[no]inter"  "no    "
 Set the next 8 options to interactive

.BI "\-[no]ss"  "no    "
 Interactive SS bridge selection

.BI "\-[no]ter"  "no    "
 Interactive termini selection, iso charged

.BI "\-[no]lys"  "no    "
 Interactive Lysine selection, iso charged

.BI "\-[no]arg"  "no    "
 Interactive Arganine selection, iso charged

.BI "\-[no]asp"  "no    "
 Interactive Aspartic Acid selection, iso charged

.BI "\-[no]glu"  "no    "
 Interactive Glutamic Acid selection, iso charged

.BI "\-[no]gln"  "no    "
 Interactive Glutamine selection, iso neutral

.BI "\-[no]his"  "no    "
 Interactive Histidine selection, iso checking H\-bonds

.BI "\-angle"  " real" " 135   " 
 Minimum hydrogen\-donor\-acceptor angle for a H\-bond (degrees)

.BI "\-dist"  " real" " 0.3   " 
 Maximum donor\-acceptor distance for a H\-bond (nm)

.BI "\-[no]una"  "no    "
 Select aromatic rings with united CH atoms on Phenylalanine, Tryptophane and Tyrosine

.BI "\-[no]ignh"  "no    "
 Ignore hydrogen atoms that are in the pdb file

.BI "\-[no]missing"  "no    "
 Continue when atoms are missing, dangerous

.BI "\-[no]v"  "no    "
 Be slightly more verbose in messages

.BI "\-posrefc"  " real" " 1000  " 
 Force constant for position restraints

.BI "\-vsite"  " enum" " none" 
 Convert atoms to virtual sites: \fB none\fR, \fB hydrogens\fR or \fB aromatics\fR

.BI "\-[no]heavyh"  "no    "
 Make hydrogen atoms heavy

.BI "\-[no]deuterate"  "no    "
 Change the mass of hydrogens to 2 amu

.BI "\-[no]chargegrp"  "yes   "
 Use charge groups in the rtp file

.BI "\-[no]cmap"  "yes   "
 Use cmap torsions (if enabled in the rtp file)

.BI "\-[no]renum"  "no    "
 Renumber the residues consecutively in the output

.BI "\-[no]rtpres"  "no    "
 Use rtp entry names as residue names

.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.
